Yes, you can remove the CD-ROM (or or original installation media) from the sources.list
Edit the sources.list file with the following command:
sudo nano /etc/apt/sources.list
And near the top, comment out the line that looks like this:
deb cdrom:[Ubuntu-Server 9.04 Jaunty Jackalope - Release i386 (20090421.1)]/ jaunty main restricted
(comment is a hash (#) - so pop one of these at the start of the deb cdrom: ... line)
Press Ctrl+X to exit the nano text editor, pressing y to save your changes
Then finally you'll need to run:
sudo apt-get update
To update your package lists.